Variant report

Variant	rs17008371
Chromosome Location	chr2:72963797-72963798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10180259	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496187	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs11126378	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11126382	0.94[AFR][1000 genomes]
rs11126386	0.94[AFR][1000 genomes]
rs11689339	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884266	0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs11886503	0.86[AFR][1000 genomes]
rs11892598	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs12614041	0.87[AFR][1000 genomes]
rs12615875	0.87[AFR][1000 genomes]
rs12619068	0.88[ASW][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs12619565	0.89[YRI][hapmap];0.93[AFR][1000 genomes]
rs1562361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008241	0.85[CEU][hapmap]
rs17008293	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs17008315	0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs17008360	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008369	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876488	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2068410	0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs4597553	0.89[YRI][hapmap];0.94[AFR][1000 genomes]
rs4852292	0.82[YRI][hapmap]
rs4852896	0.87[AFR][1000 genomes]
rs55642420	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55802296	0.84[AFR][1000 genomes]
rs56058174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56181835	0.86[AFR][1000 genomes]
rs57192957	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58890506	0.95[AFR][1000 genomes]
rs59216875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60284189	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60314340	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60584321	0.87[AFR][1000 genomes]
rs61619102	0.95[AFR][1000 genomes]
rs61736520	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6546777	0.85[YRI][hapmap]
rs66469454	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66509842	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66794803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713712	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs6716335	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs6720889	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6736649	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739768	0.85[CEU][hapmap]
rs6740390	0.84[CEU][hapmap]
rs6749495	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6754072	1.00[ASN][1000 genomes]
rs6756070	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6761253	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs67926386	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67927720	0.91[AFR][1000 genomes]
rs72846963	0.86[EUR][1000 genomes]
rs7565198	0.85[YRI][hapmap]
rs7567893	0.85[AFR][1000 genomes]
rs7586886	0.89[AFR][1000 genomes]
rs7591025	0.85[YRI][hapmap]
rs7593084	0.89[ASW][hapmap];0.98[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs7604083	0.85[CEU][hapmap]
rs7604402	0.85[YRI][hapmap]
rs7604818	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs7607226	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs764766	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17008371	CD207	cis	cerebellum	SCAN
rs17008371	TGFA	cis	cerebellum	SCAN
rs17008371	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72905800-72984400	Weak transcription	Aorta	Aorta
2	chr2:72922400-72972000	Weak transcription	Right Ventricle	heart
3	chr2:72922400-72976200	Weak transcription	Psoas Muscle	Psoas
4	chr2:72923000-72972800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:72923000-73008600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:72937200-72974200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:72937800-72978400	Weak transcription	Brain Germinal Matrix	brain
8	chr2:72938200-72987800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:72941400-72970000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:72943600-72978800	Weak transcription	Primary T cells from cord blood	blood
11	chr2:72945400-72968000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:72945600-72977800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:72946400-72974600	Weak transcription	Brain Substantia Nigra	brain
14	chr2:72946600-72969800	Weak transcription	Placenta	Placenta
15	chr2:72946600-72972800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:72946800-72971000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:72946800-72980200	Weak transcription	Left Ventricle	heart
18	chr2:72948400-72968400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:72950000-72982400	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:72950400-72970400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:72950400-72970800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:72950400-72970800	Weak transcription	NHEK	skin
23	chr2:72950400-72972600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:72951000-72970800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:72951200-72965200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:72951200-72974600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:72951400-72971400	Weak transcription	Fetal Stomach	stomach
28	chr2:72951600-72968600	Weak transcription	Small Intestine	intestine
29	chr2:72951600-72971200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:72951600-72972600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:72951800-72965200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:72951800-72967600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:72952200-72972800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:72952400-72970800	Weak transcription	Fetal Intestine Large	intestine
35	chr2:72952800-72975000	Weak transcription	Ovary	ovary
36	chr2:72953600-72970200	Weak transcription	HepG2	liver
37	chr2:72956000-72972800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:72957800-72967600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:72958400-72970800	Weak transcription	Fetal Heart	heart
40	chr2:72958600-72971200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:72958600-72975400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:72958800-72965600	Weak transcription	Fetal Lung	lung
43	chr2:72960000-72970000	Weak transcription	A549	lung
44	chr2:72960200-72970200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:72961200-72976400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:72962200-72967600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:72962600-72972800	Weak transcription	HUVEC	blood vessel

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